Sounds like a switch is going out... If I remember correctly, there's something about the wiring that could make it where if one switch goes out it can make it where the other switch associated with the window won't work either.
So, if one of the switches is being a pita, that could be your issue.
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Kinda sorta, yeah, no?
'02 Black GTP - RIP 03/03/08 ||| '06 Black G35 MT6 - Stock ||| '73 Chevy half ton(resurrected)